Fungus Fuels Tree GrowthPoplar is the fastest growing hardwood tree in the western United States, making it an energy feedstock of particular interest to the U.S. Department of Energy (DOE). The fungus is almost always found among and within poplar trees, and in an effort to understand its influence on the plant, a team of scientists studied what happens to the tree’s physical traits and gene expression when the fungus is present.

Better Genome Editing for BioenergyCRISPR-Cas9 is a powerful, high-throughput gene-editing tool that can help scientists engineer organisms for bioenergy applications. Cas9 needs guide RNA to lead it to the correct sequence to snip—but not all guides are effective. Researchers created a set of guide RNAs that were effective against 94 percent of the genes in a lipid-prolific yeast.

Cultivating Symbiotic Antarctic MicrobesIn the Proceedings of the National Academy of Sciences, researchers employed multiple microbiology and ‘omics techniques to experimentally determine that Nanohaloarchaeota are not free-living archaea but rather symbionts.

Methane Flux in the AmazonWetlands are the single largest global source of atmospheric methane. This project aims to integrate microbial and tree genetic characteristics to measure and understand methane emissions at the heart of the Amazon rainforest.

Insights into Functional Diversity in NeurosporaThis proposal investigates the genetic bases of fungal thermophily, biomass-degradation, and fungal-bacterial interactions in Sordariales, an order of biomass-degrading fungi frequently encountered in compost and encompassing one of the few groups of thermophilic fungi.

Improving the Cacao Genome and PhytozomeAn updated reference genome for Theobroma cacao Matina 1-6 has now been completed and released by HudsonAlpha scientists, with the help of Mars Wrigley funding. The annotated genome has been updated to a high quality modern standard and includes RNA-seq data. The improved genome is available for comparative purposes on the latest version of the JGI plant portal Phytozome (phytozome-next.JGI.doe.gov).

Mining IMG/M for CRISPR-Associated ProteinsResearchers report the discovery of miniature CRISPR-associated proteins that can target single-stranded DNA. The discovery was made possible by mining the datasets in the Integrated Microbial Genomes and Microbiomes (IMG/M) suite of tools managed by the JGI. The sequences were then biochemically characterized by a team led by Jennifer Doudna’s group at UC Berkeley.

What Happens Underground Influences Global Nutrient CyclesThrough the Facilities Integrating Collaborations for User Science (FICUS) program, the Environmental Molecular Sciences Laboratory (EMSL) and the DOE Joint Genome Institute (JGI) have selected 11 proposals for support from 53 received through a joint research call.

CSP Functional Genomics Call OngoingThe CSP Functional Genomics call is to enable users to perform state-of-the-art functional genomics research and to help them translate genomic information into biological function. Proposals submitted by January 31, 2019 will be part of the next review.

Learning to LookUsing machine learning, JGI researchers combed through more than 70,000 microbial and metagenome datasets, ultimately identifying more than 10,000 inovirus-like sequences compared to the 56 previously known inovirus genomes.

JGI Early Career Researchers in mSystems Special IssueJGI researchers are among the authors who offer perspectives on what the next five years of innovation could look like. In one article, Rex Malmstrom and Emiley Eloe-Fadrosh outline more targeted approaches to reconstruct individual microbes in an environmental sample. In a separate article, Simon Roux makes a pitch for readers to get involved in the developing field of virus ecogenomics.

Hidden Giants in Forest SoilsIn Nature Communications, giant virus genomes have been discovered for the first time in a forest soil ecosystem by JGI and University of Massachusetts-Amherst researchers. Most of the genomes were uncovered using a "mini-metagenomics" approach that reduced the complexity of the soil microbial communities sequenced and analyzed.

Steven Hallam, University of British Columbia

Steven Hallam, CIFAR Scholar and Associate Professor, University of British Columbia, Department of Microbiology & Immunology, Life Sciences Institute

I have collaborated with the JGI since 2002 before the CSP program came online. These collaborations have spanned my postdoctoral years with Ed DeLong [now at MIT: http://cee.mit.edu/delong] and my time as an independent investigator at the University of British Columbia. In 2002, the JGI was doing several pilot projects to explore environmental sequencing that included acid mines, eel river basin sediments and marine sponges. I worked with Nik Putnam closely on the sediment and sponge projects with some coding support from Jarrod Chapman and Sam Pitluck. (Hallam, S. J., Putnam, N. Preston, C.M., Detter, J.C., Richardson, P. M., Rokhsar, D., and E. F. DeLong. 2004. Reverse methanogenesis: testing the hypothesis with environmental genomics, Science, 305: 1457-1462. http://www.sciencemag.org/content/305/5689/1457.full)

Over the years I have worked on projects that explored the genomic potential of anaerobic methane oxidizing Archaea and the symbiotic thaumarchaeota Cenarchaeum symbiosum as well as more community based studies focused on microbial community structure and function in expanding marine oxygen minimum zones and long term soil productivity sites across north American ecozones. I have also participated in single-cell genomic studies exploring microbial dark matter from both metabolic reconstruction and technology development perspectives.

The OMZ work highlights the promise and the power of monitoring microbial communities in natural and human engineered ecosystems as sensitive indicators of change. Indeed, dissolved oxygen concentration is a critical organizing principle in the ocean. As oxygen levels decline, energy is diverted away from plants and animals into microbial community metabolism. Over the past 50 years oxygen minimum zones have expanded due to climate change and increased waste run-off from our farms and cities. At present 8% of the ocean is considered oxygen-starved. In certain coastal areas extreme oxygen-starvation produces “dead zones” decimating marine fisheries and destroying food web structure. Although inhospitable to many plants and animals, oxygen minimum zones support thriving microbial communities.

OMZ research in my laboratory has focused on the northeast subarctic Pacific Ocean and Saanich Inlet as model ecosystems for understanding microbial community responses to OMZ expansion. Using DNA and RNA extracted directly from the environment, we observed that oxygen-starvation produces alternative niches that organize and direct microbial community metabolism. Changes in microbial community metabolism in turn control marine nutrient and energy recycling, including the production and consumption of the greenhouse gases carbon dioxide, methane and nitrous oxide. We identified one specific group of microorganisms, called SUP05 related to gill symbionts of deep-sea clams and mussels that dominate the most oxygen-starved regions of the water column. SUP05 breathes-in nitrate and exhales nitrous oxide. This respiratory process is coupled to carbon dioxide fixation and the removal of toxic hydrogen sulphide. The presence of SUP05 in non-sulfidic oxygen minimum zones prompted the description of a cryptic sulphur cycle linking the metabolic activities of SUP05 with other microorganisms involved in nitrogen and sulphur cycling.

Thus, knowing how microorganisms interact with and respond to ocean oxygen starvation teaches us about the organizing principles that shape ocean food webs and define how these species work with each other and their environment in a time of climate change.

I have effectively grown up as scientist with support from the JGI. I have been exposed to cutting edge technologies and incredibly talented people that have pushed my research into unexpected and impactful places through the Community Science Program. There is no way that I could have reached this level of scientific engagement without the community sequencing program and collaborative interactions with JGI staff and the extended network of people that results from programmatic initiatives like the GEBA uncultivated project. The JGI is truly a unique human resource and an engine for innovation and discovery in genome science and systems biology.

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Check out Steven presenting in TEDxRenfrewCollingwood in Vancouver, British Columbia on October 25th, 2014.